The lessons science and pharmacology teach us about
achieving optimal health, vitality and maximal lifespan with a low net carb, high saturated fat, evolutionarily paleolithic-styled diet aligned with my ancestral heritage and how I lost 50 pounds of body fat. A sorta fairy story.

Friday, October 24, 2014

Second Episode of The Gut Guardians Podcast: "REDEFINING HUMAN" WITH JAMIE BINNS
Jamie Binns makes the 40 minute drive down to Denver to talk to Dr. Grace and Matt about Root House Studio’s newest project: Redefining Human. What better way to check out what’s going on in the gut than by looking at amazing educational videos. Thats what Root House is trying to do. But they need our help! By donating to their Kickstarter, we can help spread the word WORLDWIDE on the results being discovered via the American Gut Project.

Some topics:
--Ethnicity influence on gut health
--Matt and my experiences in recovering our gut health to tolerate dairy and gluten again
--Story of an elite athlete's gut health and new onset gluten intolerances
--Exercise and the gut; Jamie, Matt and I are all fans or fiends about exercise

This episode is jam packed with fun information about their upcoming project. Enjoy! (sorry the play button doesn't work yet, thanks for your patience!)

The purpose of these articles is to call attention to gaping holes in vaccine science, issues never before studied:

1) How childhood vaccines may affect flora balance and colonization, and

2) How existing flora (microbial predisposition) may affect vaccine response leading to injury.

The Critical Role of Microflora In Vaccine Injury

In Part 1, we explored microbes as the underlying beauty of diversity in explaining how children react differently to vaccines. It's known gut dysbiosis contributes to inflammation and poor vaccine response. This means imbalanced flora leads to vaccine failure. Children born with imbalanced flora may be prone to powerful vaccine reaction of the immune system leading to injury. Important microbes such as protective Bifidobacteria may be reduced or absent.

Some groups with microbial predisposition based on ancestral dietary habits may be predisposed to vaccine reaction and higher risk of injury. How childhood vaccines affect flora balance, short and long-term, remains unknown. And there are no studies about how the infant microbiome may predispose a child to vaccine injury.
By the CDC's own admission, African American boys may be one such group prone to vaccine injury: an increased risk of autism. One important microbial factor possibly explaining both poor vaccine response and vaccine injury is reduced or absent Bifidobacteria. Instead of doctors suggesting parents give their children Motrin or dangerous, glutathione-lowering Tylenol before and after vaccination, perhaps anti-inflammatory probiotics are in order to enhance vaccine response and protect from injury. This is the science of probiotics as vaccine adjuvants, except scientists aren't considering how probiotics may guard from injury. They're only interested in vaccine response to improve efficacy.

Before Dr. Brian Hooker's paper detailing significantly increased risk of autism by MMR vaccination in African American boys was retracted by its publisher, even stripped of its title, the Mayo Clinic was busy pondering why the African American immune system produces twice as many antibodies to the current rubella vaccine as Caucasians and Hispanics. They have no explanation other than genetics in disregard of microbial regulation of genes and immune response.

Here's Dr. Gregory Poland, head of the Mayo Clinic's Vaccine Research Group and Editor-in-Chief of the journal Vaccine, wondering aloud (video):

"The vaccine in essence is working differently. The question is, why? It's the same vaccine in human beings administered the same way and yet it stimulates a very different set of gene expression and protein secretion, that protein being antibody that protects us when we see the virus. We may be able to reduce the amount of side effects."

What Dr. Poland is not factoring is gene-microbe interaction and how people have different flora balance. Why is the Mayo Clinic focused on genes when microbiota are known to switch genes on and off, regulating geneexpression? Reducing risk of side effects may be better approached through microbial DNA testing to determine an individual's flora balance prior to vaccination.
Dr. Hooker attempts to explain the discrepancy by way of vitamin D levels, known lower in African Americans while vitamin D deficiency is pandemic not based on skin color, but flora balance. Vitamin D isn't just about sunshine as commonly touted by experts. Some studies paradoxically find vitamin D levels lowest in the brightest months. The rickets epidemic in the UK is considered a matter of low sun exposure and poor diet while beaches are polluted with sewage ten times over legal limits. Children in Bangladesh are not suffering rickets due to wearing too much sunblock. The epidemic is more likely tied to high rates of gestational diabetes leading to gut dysbiosis in newborns beginning in the womb. It's no accident all the major gut diseases include vitamin D deficiency where these diseases are matters of microbial overgrowth. Microbes make and break vitamin D. They produce precursors of the hormone, vitamin D, and the enzymes responsible for its degradation. Moreover, small intestinal malabsorption due to gut dysbiosis leads to vitamin and mineral deficiency associated with hormonal imbalance. We're only beginning to learn how gut microbiota affect hormone levels. Bifidobacteria control inflammation by way of increasinghormone-secreting endocrine cells and improving gut barrier function.
Dr. Hooker also cites a 2010 paper where the Hepatitis B vaccine administered at birth results in higher rates of autism in nonwhite boys. "Non-Hispanic white boys were 64% less likely to have autism diagnosis relative to nonwhite boys." Armed with this information, why would any doctor allow an African American male newborn HepB vaccination within 12 hours of birth per cruel CDC schedule?

And what of newborns of all races and both genders potentially predisposed to vaccine injury based on microbial predisposition? Not only are genes passed from mother to child, but so are her microbes which interact with genes. With gut imbalances and diseases such as obesity, diabetes,Celiac and Crohn's on the rise affecting future generations, we're also seeing higher rates of vaccine injury.

Microbial-gene interaction is at the core of the problem, overlooked and underappreciated. Scientists are too quick to blame genetics when addressing vaccine injury without considering how microbes turn genes on and off like light switches. It's complicated by the fact that genes also regulate flora balance, a two-way street. Microbes regulate host genes while genes regulate microbial activity. We're in this together.

Blood antigen secretor status is normally considered controlled by genes. Bifidobacteria are found significantly reduced in non-secretors where African Americans were found to have the highest percentage of non-secretors.

Gene-microbe interaction is an intracellular phenomenon not yet part of our sterile textbook landscape. The Kreb's cycle, for example, is still taught as sterile process disconnected from the web of life. There are no diagrams of the Kreb's cycle integrating intracellular microbes doing the backstroke in cytosol of cells, releasing toxins, aldehydes and free fatty acids affecting energy metabolism.

The playing field of this interaction is the gut where 70% of the body's immune system resides. So, why would African Americans produce twice the antibodies by vaccination compared to other races per Mayo Clinic?

To answer this question, let's take a close view of where these antibodies are produced in the gut,Peyer's patches and cryptopatches. This is a groundbreaking 1990 electron microscope imageof a sheep's ileum, last section of small intestine where the immune system is intimately associated with lymphatic and nervous systems, nerve bundles and fibers known as vagal afferents of thegut-brain, interface of microbes and their hosts:

The adaptive and innate immune systems work together to guide homeostasis of intestinal microbiota. But it's a two-way street as "a balanced indigenous microbiota is required to drive the normal development of both mucosa-associated lymphoid tissue, the epithelial barrier with its secretory IgA (and IgM) system." Our immune system controls flora balance by intestinal IgA and SIgA while flora controls the immune system.

Antibodies in breast milk were found to give lifelong benefit in regulating gut microbiota and gene expression while antibody excretion is enhanced by microbes such as bifidobacteria: a circle of life where antibodies control flora and flora stimulate antibodies. Breastfeeding improves vaccine response; certainly a matter of flora balance due to probiotics and prebiotics in breast milk where breastfed infant gut flora is up to 90% bifidobacteria. Might breastfeeding also decrease risk of vaccine injury?

There are several studies detailing bifidobacteria inducing antibody production, strain dependent.Bifidobacterium breve was found to increase antibodies produced in Peyer's patches as adjuvant of an oral influenza vaccine. Another bifidobacteria strain was found to activate immune response in lymphatic tissue of both small and large intestine. Bifidobacterium infantis was found protective in salmonella infection by inducing production of regulatory T-cells (Tregs). Bifidobacterium breve was tested in fermented milk, found to enhance B-cell and antibody production in Peyer's patches.

Elevated antibodies are known in autism indicating microbial imbalance and infection. For example, elevated anti-gliadin (IgG) antibodies may correlate with yeast overgrowth as gliadin is part of the fungal cell wall. Elevated measles antibodies known in autism is subject of great dispute as it may indicate abnormal immune reaction to vaccination.

The mighty Human Microbiome Project has yet to venture deeply into the small intestine, an equivalent of inner outer space. We're only beginning to understand how microbes influence health while vaccine scientists parrot age-old fallacy without evidence that children are born with sterile intestines, condoning vaccination within 12 hours of birth. Scientists are also revealing theunappreciated role of gut microbiota in immune response to vaccination. But in general, vaccine scientists have been living in a sterile world in utter disregard of microbial impact on immune response leading to injury. A particularly ominous example is high incidence of protozoans known in autism and how they may affect immune response in vaccination. Vertical, placentaltransmission of protozoans is known.

CDC protocol should be reduced and begun much later in life to allow the immune system, reliant on flora, time to develop, protecting children from injury. Microbial DNA (PCR) testing ofmeconium and routine stool testing pre-vaccination for biomarkers such as bifidobacteria may help avoid vaccine injury. An alternative is not to risk injury by vaccination, instead concentrating on building long-term natural immunity via optimal flora balance including nutrition.

How an abnormal immune reaction caused by vaccination leads to intestinal injury resulting in gut-brain malfunction such as autism will be explored in Part 3.

Monday, October 20, 2014

ROOT CAUSESSoon we'll have a special podcast interview with Jamie Binns from Root House, the producers of a new series of mini movies and a larger movie called 'REDEFINING HUMAN' and the role of our gut microbiota has on our lives, planet and health. Matt and I were really excited to talk to Jamie and find out what they are doing in the next year. Their goal is to allow normal citizens like you and I to direct and influence science by many direct interactions, contact and conversations with gut researchers. Their esteemed co-collaborators are: AmGut, U of CO Boulder and U of Chicago. Many AMA sessions (ask-me-anything) with the lead scientists will be created in the future. I suspect the public will love learning in this interactive medium.With targeted, informed research and understanding the microbiota, both medicine and healthcare with vastly change. Root causes will be better elucidated. I'm so grateful there are visionaries like Jamie and his crew at Redefining Human (because only 10% if human cells)!One of Jamie's favorite projects is personalized microbiotas -- to provide what is missing (like the ancestral core) after genetic analysis of the microbiota via AmGut or the other means available out there.The Kickstarter link is:kck.st/1tu67hA.Many levels of participation are available. I'm going for the case of kombucha UpStart for $150! yay!! Thanks Jamie for being an advocate for the humble gut microbiota, our tiny friends!!!To post direct topics, inquiries, microbiota thoughts, please leave a message or note for Jamie at his reddit:http://www.reddit.com/r/microbiology/comments/2jcbq8/were_making_a_microbiome_documentary_series_and/

Redefining Human: Science Communication Done Differently

Boulder, CO- Design firm Root House Studio and the CU: Boulder-based American Gut Project launched a Kickstarter campaign on October 15th to crowdfund a documentary series about American Gut’s revolutionary research on the human microbiome—the trillions of microbes that live in our bodies and challenge what we define as human. The aim of the series is to share information on this little known, yet incredibly important science with the general public, and to inspire the next generation of scientists to study the microbiome.

The documentary series, titled Redefining Human, will use a variety of techniques to make this complex and theoretical science easier to understand. In addition to standard documentary interviews, Root House will utilize their in-house animation team to bring to life scenes which would be nearly impossible to film, such as interactions between bacterial species and the human body. Just as the series Cosmos featuring Neil deGrasse Tyson seeks to use film and animation to explain complex scientific theories on the world beyond, Redefining Human seeks to showcase the complex world within.

Root House wants Redefining Human to be the first crowdfunded and crowdsourced science documentary series. Each episode is funded and guided by the public; using the Redefining Human Twitter andReddit pages, fans can communicate directly with the documentary team to suggest new content to cover in episodes, critique previous chapters, network with other fans, and offer ways to improve the discussion and discourse of microbiome research.

The long term goal of Root House and Redefining Human is to encourage crowdfunding as a revenue model for science communication. Since very little grant money goes towards disseminating the findings of newly-explored science, groundbreaking research on topics such as the microbiome is often doomed to remain within PhD circles. Contributions to science from billionaires such as Bill Gates, Eric Schmidt, and Lawrence Ellison have helped to push research forward (see NYT article here), but crowdfunding is poised to become the next wave that revolutionizes how science is financed.

According to Ian Scott, cofounder of Root House Studio and director of Redefining Human,

“By taking matters into their own hands, everyday citizens can fund the research that is important to them and that has a direct impact upon their lives. We want to create a community based around the crowdfunding of science, and the relevance of the microbiome makes Redefining Human a great place to start.”

Root House’s Redefining Human Kickstarter campaign began October 15th, 2014 12 pm EST. If the goal is not met within 30 days, it will not be funded. Those interested in supporting the campaign should use the link below.

For background on this project, please see the additional information provided below.

The microbiome is a 100 trillion strong army of bacteria that inhabits our bodies and redefines what we consider “human”. Almost like a microbial organ, the microbiome helps us digest food, regulates our metabolism, and fights off infection. A poorly functioning microbiome has been linked to allergies, obesity, diabetes, and immunodeficiency.

An offshoot of the Human Microbiome Project, the American Gut Project is a collaboration between the University of Colorado-Boulder and the University of Chicago. The American Gut project is mapping the human microbiome and providing open-access data analysis so scientists all over the world can begin to study how the microbiome affects our health. Already the American Gut Project has sampled over 9000 individuals and raised over $572,000 through crowdfunding/crowdswabbing efforts.

Root House is a creative studio whose mission is designing for the greater good. Based in Boulder, Colorado, Root House helps public agencies, organizations, and entrepreneurs produce the media, the aesthetic, and the delivery of their message to ensure it reaches and resonates with their target audience. Root House's designers are story tellers. They use graphics, animation, digital media, built environments and exhibits to craft compelling stories that inspire new outlooks and propel positive change.

Friday, October 17, 2014

In this episode, Grace and Matt talk about Inulin. With all the buzz around Resistant Starch, not much love is being thrown around about Inulin. By the end of this episode you’ll learn about inulin, why we can become intolerant to it, and why it’s key for feeding the right strains in our gut. Inulin proves to be key for maintaining and keeping a good flora!

Matt says that the static is still lingering in this episode, but the issue has been resolved for future episodes. Please comment or post up reviews on iTunes, we’d really appreciate it!

Autoimmune disorders: if RS eaters are in the small intestines or severe intestinal permeability continues to allow normal gut microbes to leach into the blood, don't take any resistant starch and digestible starches temporarily. How do you know? Cooked starches or raw RS make you very sick, flu-like, muscle achy, headachey, constipated, diarrhea, or bloated. Fix your gut by seeding, weeding, then feeding the missing populations of gut guardians like soil probiotics, Bifidobacteria, Roseburia and Akkermansia.

Various autoimmune disorders implicate microbes that selectively prefer digestible starch and resistant starch. Through of a process known as molecular mimicry the body mistakenly attacks its own tissues (joints, brain, bowels) in an ancient programmed attempt to contain the invading enteric microbe leaching into the blood and lymph circulation (Ebringer et al, 2011 and 2013):
--Candida
--Prevotella
--Klebsiella--Porphyromonas gingivalis
--spirochete Borrelia burgdorferi
--Serratia
--Citrobacter
--Morganella morganii (I had this one, REALLY FUN, had to SEED/WEED)--Yersinia--Shigella--Salmonella--Campylobacter--Chlamydia

Seeding with great probiotics helps crowd out weeds without toxicity or carpet bombing: Step #3 Probiotics -- soil based, bifidobacteria, lactobacilli. This includes all of our beneficial symbionts that antibiotics and high sugar diets kill off.

Ashwin Patel finds neem (Himalaya HH, TheraNeem) to be great for many gut applications: antifungal, weeding, antiparasitic/microbial, help the flow of bile, liver and skin. Tim Steele loves botanical/medicinal mushroom teas; these are potent weeders and anti-inflammatory. He's used it for many years. To blunt die-off, don't forgot charcoal, bentonite and edible earth.

After antibiotics the above adverse microbes can flourish if already present or newly introduced. Antibiotics have multiple ways of silently damaging our bodies. Antibiotics are so potent. By wiping out 'bad' flora, the collateral damage is annihilation and genocide of the 'good' microbes that are the sentinels of the gut. I like botanical ways of 'weeding' instead because these are often gentler (not always) and can preserve the gut guards like Bifidobacteria, Roseburia and Akkermansia better. The damage left by antibiotics allows the below to proliferate:
--Candida, Aspergillus, etc yeasts
--parasites (eg, E nana, I also had; B hominii, way more common than you'd think)
--protozoa (giardia, malaria, etc)
--viruses (herpes, EBV, CMV, etc)

Candida proteins resemble gluten -- once an immune reaction against candida occurs, then ginormous gluten intolerances develop. Celiac can be one if the right HLA DQ2/8 immune cells are around. The body attacks food-based wheat, barley, rye and oats with a vengeance because these contain (or are cross contaminated) with gluten. Stopping gluten allows the immune system/gut to calm down. This is Step #6 of the 7 Steps and one of the most critical.

Klebsiella pneumonia proteins resemble the collagen in joints, skin and connective tissues all over the body. If the gut is leaky and K. pneumonia breaches into the blood circulation and triggers immunity, then several inflammatory or autoimmune conditions may form. AS is an autoimmune reaction where the body attacks joints in the spine and all over the body. Klebsiella is implicated in nearly autoimmune disease including celiac disease because it is such a strong gut disruptor and opportunistic viper. The heritability and genetics of RA, celiac and other autoimmune disorders has not changed. What has changed are the mass extinctions occurring in our inner gardens. Celiacs are not born, they are created by antibiotics and the deficiency of the guardians of the gut.

The prevalence of HLA-B27 varies markedly in the general population. For example, about 8% of Caucasians, 4% of North Africans, 2-9% of Chinese, and 0.1-0.5% of persons of Japanese descent possess this gene.[1] In northern Scandinavia (Lapland), 24% of people are HLA-B27 positive, while 1.8% have associated ankylosing spondylitis. --Wikipedia

Ebringer was one of the first to promote the connection between dietary starches feeding enteric Klebsiella and several autoimmune diseases including akylosing spondylitis (AS). Klebsiella is omnivorous -- it eats both digestible and raw starches equally well. Many have failed gut issues after trying raw potato starch, HAM or even green banana flour if they have large overgrowths of Kleb, before doing some seeding and weeding. Normally the soil probiotics, Roseburia, and Bifidobacteria protect the intestinal lining to prevent this breaching of Kleb into blood circulation. High stress, sugar-refined-carb-based diets and antibiotics lower these guardians, leading to broken barriers, thus allowing Kleb, candida, Prevotella and other implicated microorganisms to breach and translocate to other organs.

"B27 disease" is a new autoimmune disease that afflicts millions of people throughout the world. "B27 disease" occurs in individuals who have ankylosing spondylitis (AS) or preankylosing spondylitis and/or uveitis and are also positive for HLA-B27. Molecular mimicry between the bowel microbe Klebsiella and the HLA-B27 molecule, as well as the spinal collagens types I, III, and IV, indicates a pathological mechanism involving autoimmunity. Antibodies to Klebsiella microbes have been reported in AS patients from 18 different countries. Sera from patients with AS show complement-dependent cytopathic activity against sheep red cells coated with HLA-B27 peptide antigens. Diagnosis of B27 disease can lead to early treatment, involving low-starch diet, sulfasalazine, and immunosuppressive and biological agents so as to prevent the irreversible bony changes of established classical AS. The concept of B27 disease provides a new approach to the study and treatment of these disorders and needs to be evaluated in prospective studies by the world rheumatological community.

Some autoimmunity will not respond well to raw potato starch or raw green banana flour. It depends if SIBO/SIFO is present -- microorganisms growing inappropriately in the small intestines -- and which organisms are growing there. If any of the listed bugs from above consume RS2, then there might be problems and worsening of autoimmunity.

IMHO Most individuals just are not that 'in tune' with their bods to identify if something is truly jiving in the gut or not. Please test, don't guess. B-I-O-H-A-C-K.

Figure out if you are low in one or many of your ancestral symbionts. Inventory an accurate list of what is in your black box, particularly if you have had or have currently an autoimmune disorder. Don't shift your gut into a shittier situation.

My favorite test is the Genova Diagnostics 2200 Stool which was recently upgraded to include some of my 7 ancestral core species. This progressive stool test will change modern medicine! Microbiome-based diagnostics and therapeutics will wipe out conventional healthcare because it offers routes to identify what's actually and truly 'wrong'.

Klebsiella appears to both consume raw RS2 and digestible starches - this is the big problem for Alkylosing Spondylitis (AS) and HLA B27.

Metabolic gut cross feeders -- I have no idea who these are but in an unhealthy, unbalanced gut, often these are present. If adverse effects occur with raw potato starch or green banana flour, then these are likely to be present. They break down RS2 to make products of starch hydrolysis, that feed one or several of the above listed pathogenic microbes.

CROWDING OUT CANDIDA, KLEBSIELLA AND/OR PREVOTELLA

To crowd out the above opportunistic vipers, try to achieve as perfect as possible digestion, probiotics and inulin to help move them out of the small intestines. A low starch diet initially helps improve Kleb, Candida or Prevotella overgrowths. The 7 steps, removing yeasts and parasites, gastric acidity and the flow of bile are all vital. Inulin (bionic fiber version B) lowers Prevotella where on the other hand raw potato starch may strongly flare it. Raising the beneficial symbionts will further eradicate any remaining vipers -- the ancestral soil probiotics, Bifidobacteria/B. longum, Roseburia and Akkermansia. These populations grow and thrive when we make a point to eat a diverse and varied rainbow of cooked-cooled RS3 and avoid high-dose raw maize or potato starch which unfortunately LOWERS ALL OF THEM. Depending on the balance and composition of organisms in the gut, high dose potato starch may worsen these gut profiles if Prevotella or Klebsiella is a dominating gut growth. Just as in high risk or pre-cancerous colorectal cancer, high dose potato starch is likely to contribute to exacerbation of a detrimental and carcinogenic gut microbiota 'fingerprint' by promoting low Roseburia and Clostridia clusters XIVa, the main butyrate factories of our guts.

7 STEPS WORKS FOR AUTOIMMUNITY

After identifying the pathogens and what beneficial gut flora are missing, it is much easier to fix autoimmunity and gut health. Here are some cases of completely resolved autoimmunity and disappearance of auto-antibodies within 4-6 weeks after starting the 7 Steps. Weeding was done to some extent in one case, but in the case only probiotics/prebiotics.

Thursday, October 9, 2014

Partnering with Mr. Matt Pepin, of RestoreTheFlora.com fame, we are launching a podcast fully focused on gut health and the microbes that make the gut its home. In the first episode we talk about why we love the gut and its importance not only in our lives, but for the future of medicine. There was even talk of the power of float tanks and zen states.

There were some technical difficulties due to Matt's old 2008 laptop. The static issue will only be present in the first two episodes.

Matt has a super funny and calm outlook on life. Like me he is a fan of his gut flora. He is also a great writer. His 12 Signs Your Flora is F*kced is my favorite post (and his first ever blog post). Ck it out!

Colorectal cancer (CRC) like all cancers is on the rise. In Australia, the prevalence is quite high and has not waned despite CSIRO launching one of the largest RS (resistant starch) campaigns to get everyone to supplement scones, cereal, muffins, rice mixes, wraps and cookies with frankenfood resistant starches like genetically hybridized BarleyMAX. Our guts are the same for the last tens of thousands of years, but the incoming food and environment are not. Parkin in Nature recently wrote about how cancer affects different parts of the world (source). CRC is in high prevalence for: orange (USA, EU, UK) 36-48%; red (AUS) 48-60% per 100,000 in males. Men and women have similar rates.

Native South Africans have the lowest CRC rates (see first digram). Their diet is rich in fermented, 'stale', whole grain-maize porridge which they sit out for a few days after making. This starchy staple is abundant in RS3 and it is estimated native Africans consume 40 to 60 grams daily RS3, and otherwise eat a relatively low 'fiber' diet of 15-25 g fiber daily.

RS3 is a network of crystallized and aggregated amyloses formed in double helical chains after 'melting' during cooking and cooling to room temp (25C) or refrigeration (4C) . The gut microbes can access RS3, but our pancreatic and salivary amylases (starch cutters) cannot. They are not 'calories' or 'carbs' in the traditional sense. They don't feed US, they feed our gut flora. Foods like maize porridge, legumes, lentils and whole grains are typically considered low glycemic index (GI). These are also the foods associated with the lowest risks of CRC in epidemiological studies across the world with estimated risk reductions of 30-81%. They are high in conventional 'fiber' and resistant starch (RS3).

Root Sources of Colorectal Cancer

More and more studies point to a microbial 'fingerprint' that characterizes CRC just as these microbial fingerprints fit nearly all other diseases of industrialized nations. According to recent examinations, guts of individuals with CRC might be described as being marked by low mucus barriers, deficiencies of big butyrate producers and overgrowths of Bacteroides. In the worst case scenarios, the mucus barriers are terribly eroded and overgrowths of even the 'good' butyrate producers have invaded. Antibiotics are the causes of many of our missing gut microbes. They wipe out the 'good' which allow opportunistic pathogens to grow in their empty niches without regulation or control. Bacteroides are overgrowing somewhere in CRC or pre-clinical stages the newest literature suggests. Bacteroides are ultra fast fermenters of RS2, raw green bananas/plantains and raw potato starch. Being omnivorous and voracious, they are involved with protein fermentation as well.

"One OTU closely related to Bacteroides fragilis was enriched in the gut microbiota of CRC patients, whereas three OTUs related to Bacteroides vulgatus and Bacteroides uniformis [ANCESTRAL CORE] were enriched in that of healthy volunteers. A total of 11 OTUs belonging to the genera Enterococcus, Escherichia/Shigella, Klebsiella, Streptococcus and Peptostreptococcus were significantly more abundant in the gut microbiota of CRC patients, and 5 OTUs belonging to the genus Roseburia and other butyrate-producing bacteria of the family Lachnospiraceae were less abundant.Reduction of butyrate producers and increase of opportunistic pathogens may constitute a major structural imbalance of gut microbiota in CRC patients."

"Partial least-squares discriminant analysis showed that 17 phylotypes closely related to Bacteroides were enriched in the gut microbiota of CRC patients, whereas nine operational taxonomic units, represented by the butyrate-producing genera Faecalibacterium and Roseburia, were significantly less abundant. A positive correlation was observed between the abundance of Bacteroides species and CRC disease status (R = 0.462, P = 0.046). In addition, 16 genera were significantly more abundant in CRC samples than in controls, including potentially pathogenic Fusobacterium and Campylobacter species at genus level. The dysbiosis of fecal microbiota, characterized by the enrichment of potential pathogens and the decrease in butyrate-producing members, may therefore represent a specific microbial signature of CRC."

Here's an example of the brand, spanking new Genova Diagnostics gut microbiota testing with 16S rRNA PCR technology. I love the new interface and it offers all the strains that I discuss. Below 'RELATIVE ABUNDANCE' is an example of low beneficial Akkermansia and high Fusobacteria, opportunistic overgrowth.

In a high dose RS2 feeding zero (control) v. 18% v. 36% high amylose maize, the big butyrate factories became reduced in abundance FIG S2 (Tachon et al 2013). Yes Bacteroides went NUTSO in growth. Recall these are overgrowing in pre-cancerous and CRC subjects. Akkermansia too, but Akkermansia is also high in CRC (due to broken mucus linings and damage from missing symbionts).

"Tachon et al state: "This reduction was most obvious for members of the families Lachnospiraceae and Ruminococceae. Lachnospiraceae represented 51 ± 14% of total bacteria in Control mice and 36 ± 14% in mice fed HAM-RS2. Similarly, Ruminococceae were reduced from 7.7 ± 4.3% of total bacteria among the Controls to 4.5 ± 2.6% in mice fed HAM-RS2. Proportions of specific Firmicutes genera were also reduced by the presence of dietary RS including Roseburia and Butyrivibrio (Fig. 3). These results were consistent with quantitative real-time PCR that showed that mice fed 36% HAM-RS2 carried lower levels of Clostridium from the clusters IV and XIV (Fig. S2).""

What does work for Lynch perhaps and other colorectal cancer prevention? How to fix root causes?

The modern, disabled gut drastically needs 'resetting' back to ancestral norms. Find a farm. Play in healthy dirt. Vigorously look at the 7 Steps and appropriate seeding/weeding, not overfeeding Bacteroides and starving out the clusters XIVa/IV (Roseburia, etc). Prior posts on Roseburia: Massive Butyrate Powerhouse.

What raises Roseburia in abundance the MOST are starches, RS3 and inulin (Van den Abeele et al 2011, others). They don't seem to like RS2. Their preference after millions of years of evolution might be related to the broad diversification of resource allocation, eg NOVEL FOOD (roasted tubers, cooked legumes). Very few strains in the gut actually have a preference to live solely on raw tuber or banana/plantain starches. All of them however eat inulin and starches. Cooked food offers much to man and their microbes. The bugs like them. Our brain and muscle metabolism likes them. Whole food also offer fiber which becomes easier to chew and assimilate after cooking and food processing.